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Related health benefits of a diet rich in organic foods include a much lower exposure to pesticides and the health risks associated with them, such as damage to the hormonal system, damage to the immune system, damage to the nervous system, birth defects, reproductive abnormalities, cancer, and declining sperm counts.

But there are several thousand naturally occurring compounds in plant foods other than vitamins and minerals. Known as phytonutrients, evidence is emerging that these compounds are the most likely reason fruits and vegetables are so health promoting, and that higher concentrations of these compounds occur in organic crops.

The benefits of phytonutrients are being increasingly documented. Many are powerful antioxidants – compounds capable of preventing unstable molecules (known as free-radicals) from causing damaging chain reactions that disrupt normal reactions in the body, burden the immune system, speed ageing processes and potentially initiate heart disease and cancer.

Why organic crops will tend to have higher concentrations of phytonutrients than conventional crops has been attributed to the fact that organic farmers are more likely to select varieties with greater resistance to pests or disease, and could thus be choosing varieties that naturally produce higher levels of phytonutrients. Many phytonutrients are produced by plants to protect themselves against attack, disease or damage. If a plant is subjected to higher levels of stress or attack it will produce more phytonutrients (Anderson 2000). So if insecticides and fungicides are reduced or avoided, a greater reliance on the plants’ own natural protection systems will result in higher phytonutrient levels.

A recent Danish literature review estimated, from the limited amount of evidence so far, that organically grown vegetables will tend to have 10–50 per cent more phytonutrients than conventionally cultivated vegetables, and concluded "if phytonutrients are an important determinant of the nutritional value of fruits and vegetables in the diet of developed countries, then vegetable and fruit products grown in organic agriculture would be expected to be more health promoting than non-organic ones" (Brandt & Mølgaard 2001).